; parse-gtf  -v 2 -i $RSAT/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.gtf -fasta $RSAT/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.dna.toplevel.fa -fasta_rm $RSAT/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.dna_rm.genome.fa -fasta_pep $RSAT/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.pep.all.fa -org_name Plasmodium_falciparum.ASM276v1.34 -task all -taxid 36329 -gtf_source ensemblgenomes -o $RSAT/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome
; Program version       	1.48
; Input files
;	fasta_rm     	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.dna_rm.genome.fa
;	fasta_pep    	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.pep.all.fa
;	fasta        	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.dna.toplevel.fa
;	gtf          	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.gtf
; Output files
;	five_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_five_prime_utr.gtf
;	tss_gtf      	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_tss.gtf
;	start_codon  	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/start_codon.tab
;	fasta_rm_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.dna_rm.genome_lengths.tab
;	contig_rm    	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/contig_rm.tab
;	stop_codon   	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/stop_codon.tab
;	gene_gtf     	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_gene.gtf
;	log          	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/log.txt
;	contigs_txt  	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/contigs.txt
;	transcript   	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/transcript.tab
;	fasta_pep_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.pep.all_lengths.tab
;	peptidic_sequences	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/peptidic_sequences.fasta
;	exon         	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/exon.tab
;	contig       	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/contig.tab
;	gene_end_gtf 	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_gene_end.gtf
;	gene_start_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_gene_start.gtf
;	transcript_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_transcript.gtf
;	gene         	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/gene.tab
;	tts_gtf      	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_tts.gtf
;	start_codon_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_start_codon.gtf
;	fasta_lengths	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34.dna.toplevel_lengths.tab
;	organism     	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/organism.tab
;	three_prime_utr_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_three_prime_utr.gtf
;	cds          	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/cds.tab
;	exon_gtf     	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_exon.gtf
;	contigs_txt_rm	/export/home1/rsat/rsat/public_html/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/contigs_rm.txt
;	stop_codon_gtf	/export/home1/rsat/rsat/data/genomes/Plasmodium_falciparum.ASM276v1.34/genome/Plasmodium_falciparum.ASM276v1.34_stop_codon.gtf
; Parsed rows per feature type
;	cds          	13914
;	exon         	14376
;	five_prime_utr	31
;	gene         	5610
;	start_codon  	5361
;	stop_codon   	5333
;	three_prime_utr	22
;	transcript   	5618
; Parsed rows per contig
;	Contig       	Total	cds	exon	five_prime_utr	gene	start	stop	three_prime_utr	transcript
;	1            	1333	348	397	0	159	135	135	0	159
;	10           	3679	1034	1035	4	401	401	400	2	402
;	11           	4621	1323	1342	7	493	479	473	6	498
;	12           	4788	1320	1332	3	539	527	525	3	539
;	13           	6515	1785	1854	0	737	702	700	0	737
;	14           	7348	2073	2101	11	804	778	772	5	804
;	2            	2096	582	587	6	231	228	223	6	233
;	3            	2290	642	658	0	252	244	242	0	252
;	4            	2276	602	678	0	263	235	235	0	263
;	5            	2908	784	828	0	335	313	313	0	335
;	6            	3053	858	880	0	336	322	321	0	336
;	7            	2731	707	771	0	332	295	294	0	332
;	8            	3025	830	878	0	341	318	317	0	341
;	9            	3602	1026	1035	0	387	384	383	0	387
; Host name	rsat01
; Job started	2017-02-27.050514
; Job done	2017-02-27.051124
; Seconds	2.98
;	user	2.98
;	system	0.15
;	cuser	360.22
;	csystem	11.88